It seems that when I make a payment through paypal it automatically defaults to taking it out of my checking account, I actually have to make a change to take it from my credit card, not sure if this was your experience or not. I will say that they (paypal) have never taken funds out of either account (checking or credit card) unless I instructed them to do so.
Beware of PayPal
I made a payment via PayPal and just noticed that they took the money out of my checking account instead of my credit card. They made this change without notifying me! Worst thing is that there's absolutely no way to contact them. They don't respond to my emails and they have no phone number to call! This is horrible!